Add joint calling documentation and pointer to write up. Fixes #348
Use bgzipped human_ancestor fasta for LOFTEE to support access with new samtools that on longer uses razip. Fixes #468
Merge pull request #635 from lpantano/upstream

add help for bcbio_setup_genome.py
Default to a reduced number of split regions (200 instead of 2000) to avoid controller memory issues with large sample sizes
Fix typo
Improve documentation of align_split_size. Fixes #636
Do not gzip fastqs for bowtie
Simple script to cleanly calculate timings from bcbio log files
Remove specific extraction of excessive coverage which doesn't provide enough removal of high coverage regions and causes issues on large populations. Thanks to @lpantano
Enable VQSR on exome analyses with 50 or more samples in a batch
Improvements for coverage: add Chanjo database to upload and correctly prepare unique name file in local directory, replacing if BED file updated
Ensure inputs to chanjo are cleaned and sorted, attempting to avoid issues identified by @lbeltrame
Use vt normalization instead of bcftools normalization to attempt to avoid segmentation faults #639
Add Alla's link to repo. Remove .travis.yml
Merge pull request #641 from guillermo-carrasco/brad_master

Missing link to Alla Bushoy's repo
Enable small validation plots with restricted columns when data is missing
Provide improved uniqueness of shared temporary transactional directories. Use fully random UUIDs and check for conflicts. Fixes #642
Talk for Boston area bioinformatics interest group (BIG) meeting
Correctly handle pre-aligned inputs when GATK not installed. Thanks to Stephan Pabinger
Fix samtools output to be compatible with tools that cannot handle VCFv4.2